Understanding mirroring and inverting an object
The mirror tool (CTRLM) actually inverts the model by scaling it -1. This will flip the model, but will also invert the normals.

Here's what the docs say:


  The mirror tool in Edit mode is similar to Mirroring in Object mode.
  It is exactly equivalent to scaling by -1 vertices, edges or faces
  around one chosen pivot point and in the direction of one chosen axis,
  only it is faster/handier.


I'm not exactly sure what the mirror modifier is doing, but I'm assuming it copies the vertices location along the axis and puts it in the negative location. Here's what the docs say:


  The Mirror modifier automatically mirrors a mesh along its local X, Y
  and/or Z axes, which pass through the object’s center (the mirror
  plane is then defined by the two other axes).